This wouldn't work because $$ would be the same for every instance of the system call. Since the code is using a for loop, try using the counter variable to uniquely name the files:

system("myscript.prl $id > $tmp_file$i");
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/\/\averick
perl -l -e "eval pack('h*','072796e6470272f2c5f2c5166756279636b672');"